def test_group_kind():
group = Group("arbitrary_group1")
with pytest.raises(ValueError) as excinfo:
group.kind = "non-SBML compliant group kind"
assert "Kind can only by one of:" in str(excinfo.value)
group.kind = "collection"
assert group.kind == "collection"
def test_group_kind():
group = Group("arbitrary_group1")
with pytest.raises(ValueError) as excinfo:
group.kind = "non-SBML compliant group kind"
assert "Kind can only by one of:" in str(excinfo.value)
group.kind = "collection"
assert group.kind == "collection"
def test_copy_with_groups(model):
sub = Group("pathway", members=[model.reactions.PFK, model.reactions.FBA])
model.add_groups([sub])
copy = model.copy()
assert len(copy.groups) == len(model.groups)
assert len(copy.groups.get_by_id("pathway")) == len(
model.groups.get_by_id("pathway"))
def test_group_members_add_to_model(model):
# remove a few reactions from the model and add them to a new group
num_members = 5
reactions_for_group = model.reactions[0:num_members]
model.remove_reactions(reactions_for_group, remove_orphans=False)
group = Group("arbitrary_group1")
group.add_members(reactions_for_group)
group.kind = "collection"
# the old reactions should not be in the model
for reaction in reactions_for_group:
assert reaction not in model.reactions
# add the group to the model and check that the reactions were added
model.add_groups([group])
assert group in model.groups
for reaction in reactions_for_group:
assert reaction in model.reactions
def test_group_members_add_to_model(model):
# remove a few reactions from the model and add them to a new group
num_members = 5
reactions_for_group = model.reactions[0:num_members]
model.remove_reactions(reactions_for_group, remove_orphans=False)
group = Group("arbitrary_group1")
group.add_members(reactions_for_group)
group.kind = "collection"
# the old reactions should not be in the model
for reaction in reactions_for_group:
assert reaction not in model.reactions
# add the group to the model and check that the reactions were added
model.add_groups([group])
assert group in model.groups
for reaction in reactions_for_group:
assert reaction in model.reactions
def test_group_loss_of_elements(model):
# when a metabolite, reaction, or gene is removed from a model, it
# should no longer be a member of any groups
num_members_each = 5
elements_for_group = model.reactions[0:num_members_each]
elements_for_group.extend(model.metabolites[0:num_members_each])
elements_for_group.extend(model.genes[0:num_members_each])
group = Group("arbitrary_group1")
group.add_members(elements_for_group)
group.kind = "collection"
model.add_groups([group])
remove_met = model.metabolites[0]
model.remove_metabolites([remove_met])
remove_rxn = model.reactions[0]
model.remove_reactions([remove_rxn])
remove_gene = model.genes[0]
remove_gene.remove_from_model()
assert remove_met not in group.members
assert remove_rxn not in group.members
assert remove_gene not in group.members
def test_group_loss_of_elements(model):
# when a metabolite, reaction, or gene is removed from a model, it
# should no longer be a member of any groups
num_members_each = 5
elements_for_group = model.reactions[0:num_members_each]
elements_for_group.extend(model.metabolites[0:num_members_each])
elements_for_group.extend(model.genes[0:num_members_each])
group = Group("arbitrary_group1")
group.add_members(elements_for_group)
group.kind = "collection"
model.add_groups([group])
remove_met = model.metabolites[0]
model.remove_metabolites([remove_met])
remove_rxn = model.reactions[0]
model.remove_reactions([remove_rxn])
remove_gene = model.genes[0]
remove_gene.remove_from_model()
assert remove_met not in group.members
assert remove_rxn not in group.members
assert remove_gene not in group.members
def test_group_model_reaction_association(model):
num_members = 5
reactions_for_group = model.reactions[0:num_members]
group = Group("arbitrary_group1")
group.add_members(reactions_for_group)
group.kind = "collection"
model.add_groups([group])
# group should point to and be associated with the model
assert group._model is model
assert group in model.groups
# model.get_associated_groups should find the group for each reaction
# we added to the group
for reaction in reactions_for_group:
assert group in model.get_associated_groups(reaction)
# remove the group from the model and check that reactions are no
# longer associated with the group
model.remove_groups([group])
assert group not in model.groups
assert group._model is not model
for reaction in reactions_for_group:
assert group not in model.get_associated_groups(reaction)
def test_group_model_reaction_association(model):
num_members = 5
reactions_for_group = model.reactions[0:num_members]
group = Group("arbitrary_group1")
group.add_members(reactions_for_group)
group.kind = "collection"
model.add_groups([group])
# group should point to and be associated with the model
assert group._model is model
assert group in model.groups
# model.get_associated_groups should find the group for each reaction
# we added to the group
for reaction in reactions_for_group:
assert group in model.get_associated_groups(reaction)
# remove the group from the model and check that reactions are no
# longer associated with the group
model.remove_groups([group])
assert group not in model.groups
assert group._model is not model
for reaction in reactions_for_group:
assert group not in model.get_associated_groups(reaction)
def test_group_add_elements(model):
num_members = 5
reactions_for_group = model.reactions[0:num_members]
group = Group("arbitrary_group1")
group.add_members(reactions_for_group)
group.kind = "collection"
# number of member sin group should equal the number of reactions
# assigned to the group
assert len(group.members) == num_members
# Choose an overlapping, larger subset of reactions for the group
num_total_members = 12
reactions_for_larger_group = model.reactions[0:num_total_members]
group.add_members(reactions_for_larger_group)
assert len(group.members) == num_total_members
def test_group_add_elements(model):
num_members = 5
reactions_for_group = model.reactions[0:num_members]
group = Group("arbitrary_group1")
group.add_members(reactions_for_group)
group.kind = "collection"
# number of member sin group should equal the number of reactions
# assigned to the group
assert len(group.members) == num_members
# Choose an overlapping, larger subset of reactions for the group
num_total_members = 12
reactions_for_larger_group = model.reactions[0:num_total_members]
group.add_members(reactions_for_larger_group)
assert len(group.members) == num_total_members